urika 0.1.0__tar.gz

urika-0.1.0/.github/workflows/workflow.yml

@@ -0,0 +1,51 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  id-token: write
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build tools
+        run: pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/urika
+    permissions:
+      id-token: write
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

urika-0.1.0/.gitignore

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+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+dist/
+build/
+.eggs/
+*.egg
+.pytest_cache/
+.ruff_cache/
+*.so
+.venv/
+venv/
+env/
+.env
+*.db
+.worktrees/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Urika project data (not part of the repo)
+urika-projects/
+
+# Test dataset downloads (configs and knowledge ARE tracked)
+dev/test-datasets/*/data/

urika-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to Urika will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1.0] - 2026-03-30
+
+Initial pre-release.
+
+### Added
+
+- Multi-agent orchestration system with 11 specialized agent roles
+- Experiment lifecycle: planning, task execution, evaluation, advisory loop
+- Meta-orchestrator for autonomous multi-experiment campaigns
+- Finalization sequence: standalone methods, findings, reports, presentations
+- 18 built-in statistical and ML tools
+- Knowledge pipeline with PDF, text, and URL extractors
+- Interactive REPL with 25+ slash commands
+- CLI with 20+ commands
+- Notification system (Email, Slack, Telegram) with remote control
+- Pause/stop/resume for experiments and multi-experiment runs
+- Reveal.js presentation generation
+- Project builder with data profiling and multi-format support
+- Versioned criteria system with advisor-driven evolution
+- Method registry tracking all approaches across experiments
+- Auto-generated labbooks, reports, and README files
+- Privacy-aware hybrid endpoint model (public/private)
+- 1072 tests

urika-0.1.0/LICENSE

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urika-0.1.0/PKG-INFO

@@ -0,0 +1,257 @@
+Metadata-Version: 2.4
+Name: urika
+Version: 0.1.0
+Summary: Multi-agent scientific analysis platform
+License-Expression: Apache-2.0
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.11
+Requires-Dist: claude-agent-sdk>=0.1
+Requires-Dist: click>=8.0
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=2.0
+Requires-Dist: pingouin>=0.5
+Requires-Dist: prompt-toolkit>=3.0
+Requires-Dist: pypdf>=4.0
+Requires-Dist: scikit-learn>=1.3
+Requires-Dist: scipy>=1.11
+Requires-Dist: seaborn>=0.13
+Requires-Dist: statsmodels>=0.14
+Provides-Extra: all
+Requires-Dist: imbalanced-learn>=0.11; extra == 'all'
+Requires-Dist: lightgbm>=4.0; extra == 'all'
+Requires-Dist: optuna>=3.0; extra == 'all'
+Requires-Dist: python-telegram-bot>=20.0; extra == 'all'
+Requires-Dist: sentence-transformers>=2.2; extra == 'all'
+Requires-Dist: shap>=0.42; extra == 'all'
+Requires-Dist: slack-sdk>=3.0; extra == 'all'
+Requires-Dist: timm>=0.9; extra == 'all'
+Requires-Dist: torch>=2.0; extra == 'all'
+Requires-Dist: torchaudio>=2.0; extra == 'all'
+Requires-Dist: torchvision>=0.15; extra == 'all'
+Requires-Dist: transformers>=4.30; extra == 'all'
+Requires-Dist: xgboost>=2.0; extra == 'all'
+Provides-Extra: dev
+Requires-Dist: imbalanced-learn>=0.11; extra == 'dev'
+Requires-Dist: lightgbm>=4.0; extra == 'dev'
+Requires-Dist: optuna>=3.0; extra == 'dev'
+Requires-Dist: pytest-asyncio>=0.23; extra == 'dev'
+Requires-Dist: pytest>=7.0; extra == 'dev'
+Requires-Dist: python-telegram-bot>=20.0; extra == 'dev'
+Requires-Dist: ruff>=0.1; extra == 'dev'
+Requires-Dist: sentence-transformers>=2.2; extra == 'dev'
+Requires-Dist: shap>=0.42; extra == 'dev'
+Requires-Dist: slack-sdk>=3.0; extra == 'dev'
+Requires-Dist: timm>=0.9; extra == 'dev'
+Requires-Dist: torch>=2.0; extra == 'dev'
+Requires-Dist: torchaudio>=2.0; extra == 'dev'
+Requires-Dist: torchvision>=0.15; extra == 'dev'
+Requires-Dist: transformers>=4.30; extra == 'dev'
+Requires-Dist: xgboost>=2.0; extra == 'dev'
+Provides-Extra: dl
+Requires-Dist: sentence-transformers>=2.2; extra == 'dl'
+Requires-Dist: timm>=0.9; extra == 'dl'
+Requires-Dist: torch>=2.0; extra == 'dl'
+Requires-Dist: torchaudio>=2.0; extra == 'dl'
+Requires-Dist: torchvision>=0.15; extra == 'dl'
+Requires-Dist: transformers>=4.30; extra == 'dl'
+Provides-Extra: ml
+Requires-Dist: imbalanced-learn>=0.11; extra == 'ml'
+Requires-Dist: lightgbm>=4.0; extra == 'ml'
+Requires-Dist: optuna>=3.0; extra == 'ml'
+Requires-Dist: shap>=0.42; extra == 'ml'
+Requires-Dist: xgboost>=2.0; extra == 'ml'
+Provides-Extra: notifications
+Requires-Dist: python-telegram-bot>=20.0; extra == 'notifications'
+Requires-Dist: slack-sdk>=3.0; extra == 'notifications'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <img src="docs/assets/header.png" alt="Urika" width="580">
+</p>
+
+<p align="center">
+  <a href="docs/01-getting-started.md">Getting Started</a> &middot;
+  <a href="docs/09-agent-system.md">Agent System</a> &middot;
+  <a href="docs/12-models-and-privacy.md">Models &amp; Privacy</a> &middot;
+  <a href="docs/17-notifications.md">Notifications</a> &middot;
+  <a href="docs/15-cli-reference.md">CLI Reference</a> &middot;
+  <a href="docs/16-interactive-repl.md">Interactive REPL</a>
+</p>
+
+---
+
+> **Early Development** — Urika is under active development. Expect frequent updates, bug fixes, and new features. Check back regularly or run `urika setup` to see if a new version is available. Bug reports and feedback welcome at [GitHub Issues](https://github.com/xkiwilabs/Urika/issues).
+
+Urika uses multiple AI agents to autonomously explore analytical approaches for your dataset and research question. It creates experiments, tries different methods, evaluates results, searches relevant literature, and builds custom tools when needed. Everything is documented automatically — experiment labbooks, project-level reports, key findings, and slide presentations you can view in any browser. Each experiment's methods, metrics, and observations are tracked in structured records that agents use to plan the next step.
+
+Currently supports the **Claude Agent SDK** (Anthropic), including local models via Ollama. Adapters for **OpenAI Agents SDK**, **Google Agent Development Kit (ADK)**, and **PI** are planned for upcoming releases.
+
+**Runs on Linux, macOS, and Windows 11.** For local/private model setups (Ollama, vLLM, LiteLLM), see [Models & Privacy](docs/12-models-and-privacy.md).
+
+## Installation
+
+### Prerequisites
+
+1. Python >= 3.11
+2. Claude Pro or Max account (recommended) — or an Anthropic API key
+3. Claude Code CLI — install and log in first:
+
+```bash
+npm install -g @anthropic-ai/claude-code
+claude login                    # opens browser to authenticate
+```
+
+### Install Urika
+
+```bash
+pip install urika
+urika setup                     # check installation, detect hardware, optionally install DL
+```
+
+The default install includes visualization, ML, statistics, knowledge pipeline, and notification support. Deep learning (torch, transformers) is optional: `pip install "urika[dl]"`.
+
+**From source (development):**
+
+```bash
+git clone https://github.com/xkiwilabs/Urika.git
+cd Urika
+pip install -e ".[dev]"
+```
+
+See [Getting Started](docs/01-getting-started.md) for full details.
+
+## Quickstart
+
+```bash
+urika new my-study --data ./my_data.csv    # create a project (interactive)
+urika run my-study                          # run experiments
+urika finalize my-study                     # produce final report
+urika                                       # or use the interactive REPL
+```
+
+See the [Getting Started](docs/01-getting-started.md) guide for a full walkthrough.
+
+## How It Works
+
+```mermaid
+flowchart TD
+    A["urika new\nProject Builder"] --> B["Scans data, profiles,\ningests knowledge"]
+    B --> C{"How to run?"}
+
+    C -- "Single experiment\n(guided)" --> D["urika run"]
+    C -- "Multiple experiments\n(autonomous)" --> META["urika run --max-experiments N\nAutonomous Mode"]
+
+    D --> LOOP
+    META --> LOOP
+
+    subgraph LOOP ["Experiment Loop (per experiment)"]
+        direction TB
+        P["Planning Agent\ndesigns method"] --> TA["Task Agent\nwrites code, runs tools"]
+        TA --> EV["Evaluator\nscores against criteria"]
+        EV --> Q{Criteria met?}
+        Q -- No --> ADV["Advisor Agent\nanalyzes, proposes next"]
+        ADV --> P
+        Q -- "Yes\n(--review-criteria)" --> RC["Advisor reviews\ncriteria"]
+        RC -- "raises bar" --> P
+        RC -- "confirms" --> REPORT
+        Q -- Yes --> REPORT["Generate Reports"]
+    end
+
+    D -- "after experiment" --> REVIEW["User reviews results\ndecides next step"]
+    REVIEW -- "run again" --> D
+
+    META -- "advisor decides\nnext experiment" --> LOOP
+
+    REPORT --> FIN["urika finalize\nFinalizer Agent"]
+    FIN --> OUT["Standalone methods\nFinal report & presentation\nReproduce scripts"]
+
+    TA -. "needs tool" .-> TB["Tool Builder"]
+    P -. "needs literature" .-> LIT["Literature Agent"]
+    TB -.-> TA
+    LIT -.-> P
+```
+
+Eleven agents work together. Each experiment runs autonomously — agents plan, execute, evaluate, and iterate without intervention. You choose how to manage the *between-experiment* flow:
+
+- **Guided** (`urika run`) — agents run one experiment autonomously, then you review results and decide what to try next. Best for exploratory work and complex domains where human judgment matters between experiments.
+- **Fully autonomous** (`urika run --max-experiments N`) — the system runs multiple experiments back-to-back, with the advisor agent deciding what to try next. Best when you've provided detailed context (see [Prompts and Context](docs/04-prompts-and-context.md)).
+
+Within each experiment, the orchestrator cycles through `planning -> task -> evaluator -> advisor` each turn. When all experiments are complete, the **Finalizer** produces standalone deliverables.
+
+See [Agent System](docs/09-agent-system.md) for details on each agent role.
+
+## Scriptable CLI
+
+Every Urika command is fully scriptable -- pass arguments and flags directly, get structured JSON output with `--json`, and chain commands in shell scripts. No interactive prompts when flags are provided.
+
+```bash
+# Create and run a project in one script
+urika new my-study --data ~/data/scores.csv --question "What predicts outcome?" --mode exploratory
+urika run my-study --max-turns 5 --instructions "focus on tree-based models"
+urika run my-study --max-experiments 3 --auto
+urika finalize my-study --instructions "emphasize the best model"
+
+# Get structured output for custom tooling
+urika status my-study --json
+urika results my-study --json
+urika methods my-study --json
+
+# Remote control via Telegram/Slack while experiments run
+# See Notifications docs for setup
+```
+
+This makes it straightforward to build custom workflows, batch processing scripts, CI pipelines, or wrap Urika in your own research tools. See [CLI Reference](docs/15-cli-reference.md) for the full command list.
+
+## Privacy and Model Configuration
+
+Each project can configure which models and endpoints its agents use. Three privacy modes:
+
+- **Open** (default) -- all agents use cloud models via API. No restrictions.
+- **Private** -- all agents use private endpoints only. This can be local models (Ollama), a secure institutional server, or any combination -- whatever stays within your data governance boundary.
+- **Hybrid** -- a private Data Agent reads raw data and outputs sanitized summaries; all other agents run on cloud models for maximum analytical power. Raw data never leaves your private environment. The default hybrid split covers most cases, but you can customize which agents use which endpoints to ensure what needs to be private stays private.
+
+Per-agent model routing lets you optimize for cost (Haiku for simple tasks, Opus for complex reasoning) or compliance (institutional servers for data access, cloud for method design). Different projects can have completely different privacy and model settings.
+
+See above for supported and upcoming SDK adapters.
+
+See [Models and Privacy](docs/12-models-and-privacy.md) for configuration details.
+
+## Documentation
+
+| Guide | Description |
+|-------|-------------|
+| [Getting Started](docs/01-getting-started.md) | Installation, requirements, first project |
+| [Core Concepts](docs/02-core-concepts.md) | Projects, experiments, runs, methods, tools, agents |
+| [Creating Projects](docs/03-creating-projects.md) | `urika new`, data scanning, knowledge ingestion |
+| [Prompts and Context](docs/04-prompts-and-context.md) | Writing effective descriptions, instructions, knowledge ingestion |
+| [Running Experiments](docs/05-running-experiments.md) | Orchestrator loop, turns, auto mode, resume |
+| [Advisor Chat and Instructions](docs/06-advisor-and-instructions.md) | Standalone advisor conversations, steering agents, suggestion-to-run flow |
+| [Viewing Results](docs/07-viewing-results.md) | Reports, presentations, methods, leaderboard |
+| [Finalizing Projects](docs/08-finalizing-projects.md) | Finalization sequence, standalone methods, reproducibility |
+| [Agent System](docs/09-agent-system.md) | All 11 agent roles and how they interact |
+| [Built-in Tools](docs/10-built-in-tools.md) | 18 analysis tools agents use |
+| [Knowledge Pipeline](docs/11-knowledge-pipeline.md) | Ingesting papers, PDFs, searching |
+| [Models and Privacy](docs/12-models-and-privacy.md) | Per-agent model routing, endpoints, hybrid privacy mode |
+| [Configuration](docs/13-configuration.md) | urika.toml, criteria, preferences |
+| [Project Structure](docs/14-project-structure.md) | File layout and what each file does |
+| [CLI Reference](docs/15-cli-reference.md) | Every command with full options |
+| [Interactive REPL](docs/16-interactive-repl.md) | Slash commands, tab completion, conversation mode |
+| [Notifications](docs/17-notifications.md) | Email, Slack, Telegram alerts and remote commands |
+
+## Citation
+
+If you use Urika in your research or analysis, please acknowledge its use in your publications:
+
+> Urika -- Multi-agent scientific analysis platform. Developed by Michael J. Richardson and colleagues at Macquarie University, Sydney, Australia. https://github.com/xkiwilabs/Urika
+
+## License
+
+[Apache 2.0](LICENSE) -- Free to use, modify, and distribute for any purpose, including commercial use. Includes patent protection for contributors. See the [full license](LICENSE) for details.